Ž . Biochimica et Biophysica Acta 1385 1998 107–114 Theoretical evidence of the existence of a diazafulvene intermediate in the reaction pathway of imidazoleglycerol phosphate dehydratase: design of a novel and potent heterocycle structure for the inhibitor on the basis of the electronic structure-activity relationship study Keigo Gohda a, ),1 , Yoko Kimura b,2 , Ichiro Mori b,3 , Daisaku Ohta c,4 , Takeshi Kikuchi a,5 a Computer Chemistry Unit, International Research Laboratories, CIBA-GEIGY Japan, P.O. Box 1, Takarazuka, Hyogo 665, Japan b Chemistry Department, International Research Laboratories, CIBA-GEIGY Japan, P.O. Box 1, Takarazuka, Hyogo 665, Japan c Bio-organic Research Department, International Research Laboratories, CIBA-GEIGY Japan, P.O. Box 1, Takarazuka, Hyogo 665, Japan Received 20 February 1998; accepted 13 March 1998 Abstract The reaction mechanism of imidazoleglycerol phosphate dehydratase has not yet been clearly revealed. Structural comparison between inhibitors and the substrate IGP implicates that the reaction involves a diazafulvene intermediate. Here, we present evidence to support this hypothesis by investigating the electronic structure-enzyme inhibitory activity relationship on inhibitors with different heterocycles using 6-31G)) level theory of the ab initio molecular orbital method. The calculation results showed that potent inhibitors can be distinguished from weak ones by the atomic charge density and by the energy levels of the highest occupied lone-pair orbital on the nitrogen atoms in the heterocycles. Furthermore, very Ž 2 . good correlations r s 0.8–0.9 were found between the charge density on the nitrogen atom and the inhibitory activity. It was also revealed that the diazafulvene is electronically similar to the potent inhibitors. Thus, these results strongly suggest the existence of the diazafulvene as an intermediate possessing tight-binding affinity to the enzyme. Based on the electronic structural similarity between the potent inhibitors and the proposed intermediate, a novel heterocycle was designed and predicted its inhibitory activity prior to the synthesis. Then, activity of synthesized inhibitors showed excellent agreement with this prediction. Hence, from the theoretical studies and experimental results, we conclude to obtain evidence of the hypothesis that the enzyme reaction proceeds via the diazafulvene intermediate. q 1998 Elsevier Science B.V. All rights reserved. Keywords: Diazafulvene; Enzyme inhibitor; Imidazoleglycerol phosphate dehydratase; Reaction intermediate; Structure-activity relation- ship study Abbreviations: F, the value from F-test; MO, molecular orbital; r 2 , squared correlation coefficient; SD, the standard deviation ) Corresponding author. Fax: q81-797-74-2598; E-mail: keigo.gohda@pharma.novartis.com 1 Present address: Research Department, Novartis Pharma K. K., P.O. Box 1, Takarazuka, Hyogo 665, Japan. 2 Present address: Univ. of Occupational and Environmental Health, 1-1, Iseigaoka, Yahata-nishi-ku, Kitakyushu, Fukuoka 807, Japan. 3 Present address: Research Department, Novartis Pharma K.K., P.O. Box 1, Takarazuka, Hyogo 665, Japan. 4 Present address: Research Institute for Biological Sciences, Okayama, 7549-1 Yoshikawa, Kayo-cho, Okayama 716-12, Japan. 5 Present address: Frontier Research Center for Computational Sciences, Science Univ. of Tokyo, 2641 Yamasaki, Noda, Chiba 278, Japan. 0167-4838r98r$19.00 q 1998 Elsevier Science B.V. All rights reserved. Ž . PII S0167-4838 98 00049-1